Chromosomes, and genomes in general, are generally believed to be organized in three dimensions such that functionally related genomic elements, e.g. enhancers and their target genes, are directly interacting or are located in very close spatial proximity. Such close physical proximity between genomic elements has been reported to play a role in genome biology both in normal development and homeostasis and in disease.
Genomes are believed to be multicompositional complexes comprising of mainly nucleic acids and proteins. Polymers of both biological building blocks have primary, secondary, and tertiary conformational structure. For example, a primary conformational structure is believed to be represented by a linear sequence of individual nucleotides, thereby forming a polynucleotide or a linear sequence of individual amino acids, thereby forming a protein (i.e., includes the first dimension).
On the other hand, both secondary and tertiary conformational structures describe torsional considerations of the polynucleotide or protein in response to the ionic charges and steric interactions of the various chemical moieties that make up the primary sequences. Secondary structure is related to twisting and turning relative to the longitudinal axis of the polymer (i.e., includes the first and second dimensions). Tertiary structure is related to folding and looping of the polymer (i.e., includes the first, second and third dimensions).
What is needed in the art is a method by which direct intra- and interchromosomal interactions between remote regulatory elements, or spatial proximity of these elements, may be identified in a comprehensive manner and utilized to diagnose specific medical and/or biological conditions.